Measuring Surface area TMA

Hi all,

I’m currently trying to get a grasp of qupath and what it can do, using the tutorials ect.
However, I was not able to find how to measure the percentage of a DAB+ surface (/cells) in a TMA core compared to the total surface area of the core without doing cell segmentation.
Did I overlook something? Or isn’t this feasible and should I go for segmentation?

Many thanks in advance!

Kind regards,

Which version of QuPath are you using? How precise do you need to be/how small of stained objects do you need to pick up?

Have you tried the Pixel classifier in M9, or the Positive Pixel Detection in 0.1.2?
Some options from an old guide: QuPath Intro: Choose your own analysis(adventure)

I am not sure if there is a “Pixel classifier” post at this time, but there are quite a few posts scattered around the forum relating to other people using it if you look.

Guide on using SLICs in the earlier versions of QuPath.

  • once you have something working, it will probably need to be altered to work in a TMA format. Simple tissue detection CAN be run on a TMA grid, however, and there are scripts to name the annotations after their TMA grid location.